1-94047009-C-T

Position:

chr1-94047009-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 4P and 13B. PM1PM5BP4_StrongBP6BS1BS2

The NM_000350.3(ABCA4):c.2828G>A(p.Arg943Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0406 in 1,614,062 control chromosomes in the GnomAD database, including 1,540 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R943G) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.029 ( 98 hom., cov: 32)

Exomes 𝑓: 0.042 ( 1442 hom. )

Consequence

ABCA4
NM_000350.3 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:3U:1B:16O:2

Conservation

PhyloP100: 1.07

Variant links:

Genes affected

ABCA4 (HGNC:34): (ATP binding cassette subfamily A member 4) The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. This protein is a retina-specific ABC transporter with N-retinylidene-PE as a substrate. It is expressed exclusively in retina photoreceptor cells, and the gene product mediates transport of an essental molecule, all-trans-retinal aldehyde (atRAL), across the photoreceptor cell membrane. Mutations in this gene are found in patients diagnosed with Stargardt disease, a form of juvenile-onset macular degeneration. Mutations in this gene are also associated with retinitis pigmentosa-19, cone-rod dystrophy type 3, early-onset severe retinal dystrophy, fundus flavimaculatus, and macular degeneration age-related 2. [provided by RefSeq, Sep 2019]

ABCA4 links:

ABCA4 (HGNC:):

ABCA4 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

PM1

In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 9 uncertain in NM_000350.3

PM5

Other missense variant is known to change same aminoacid residue: Variant chr1-94047010-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 99162.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP4

Computational evidence support a benign effect (MetaRNN=0.0059529543).

BP6

Variant 1-94047009-C-T is Benign according to our data. Variant chr1-94047009-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 7913.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=7, Established_risk_allele=1, not_provided=1, Benign=6}. Variant chr1-94047009-C-T is described in Lovd as [Likely_pathogenic]. Variant chr1-94047009-C-T is described in Lovd as [Likely_benign]. Variant chr1-94047009-C-T is described in Lovd as [Benign]. Variant chr1-94047009-C-T is described in Lovd as [Pathogenic]. Variant chr1-94047009-C-T is described in Lovd as [Pathogenic].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0291 (4430/152184) while in subpopulation NFE AF= 0.0433 (2942/68002). AF 95% confidence interval is 0.042. There are 98 homozygotes in gnomad4. There are 2120 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 98 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCA4	NM_000350.3 linkuse as main transcript	c.2828G>A	p.Arg943Gln	missense_variant	19/50	ENST00000370225.4	NP_000341.2	P78363Q6AI28
ABCA4	XM_047416704.1 linkuse as main transcript	c.2606G>A	p.Arg869Gln	missense_variant	18/49

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCA4	ENST00000370225.4 linkuse as main transcript	c.2828G>A	p.Arg943Gln	missense_variant	19/50	1	NM_000350.3	ENSP00000359245.3		P78363
ABCA4	ENST00000649773.1 linkuse as main transcript	c.2606G>A	p.Arg869Gln	missense_variant	18/19			ENSP00000496882.1		A0A3B3IRV8

Frequencies

GnomAD3 genomes

AF:

0.0291

AC:

4428

AN:

152066

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0118

Gnomad AMI

AF:

0.0319

Gnomad AMR

AF:

0.0202

Gnomad ASJ

AF:

0.0202

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0422

Gnomad FIN

AF:

0.0298

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0433

Gnomad OTH

AF:

0.0301

GnomAD3 exomes

AF:

0.0302

AC:

7592

AN:

251410

Hom.:

163

AF XY:

0.0322

AC XY:

4376

AN XY:

135874

show subpopulations

Gnomad AFR exome

AF:

0.0104

Gnomad AMR exome

AF:

0.0117

Gnomad ASJ exome

AF:

0.0212

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.0419

Gnomad FIN exome

AF:

0.0317

Gnomad NFE exome

AF:

0.0408

Gnomad OTH exome

AF:

0.0314

GnomAD4 exome

AF:

0.0418

AC:

61092

AN:

1461878

Hom.:

1442

Cov.:

AF XY:

0.0416

AC XY:

30260

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.0109

Gnomad4 AMR exome

AF:

0.0121

Gnomad4 ASJ exome

AF:

0.0200

Gnomad4 EAS exome

AF:

0.000227

Gnomad4 SAS exome

AF:

0.0419

Gnomad4 FIN exome

AF:

0.0338

Gnomad4 NFE exome

AF:

0.0466

Gnomad4 OTH exome

AF:

0.0367

GnomAD4 genome

AF:

0.0291

AC:

4430

AN:

152184

Hom.:

Cov.:

AF XY:

0.0285

AC XY:

2120

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.0118

Gnomad4 AMR

AF:

0.0202

Gnomad4 ASJ

AF:

0.0202

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0426

Gnomad4 FIN

AF:

0.0298

Gnomad4 NFE

AF:

0.0433

Gnomad4 OTH

AF:

0.0298

Alfa

AF:

0.0359

Hom.:

165

Bravo

AF:

0.0269

TwinsUK

AF:

0.0464

AC:

172

ALSPAC

AF:

0.0439

AC:

169

ESP6500AA

AF:

0.0143

AC:

ESP6500EA

AF:

0.0410

AC:

353

ExAC

AF:

0.0307

AC:

3724

Asia WGS

AF:

0.0260

AC:

AN:

3478

EpiCase

AF:

0.0405

EpiControl

AF:

0.0421

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:3Uncertain:1Benign:16Other:2

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not specified

Benign:6

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 12, 2011	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Nov 26, 2013	- -

not provided

Benign:3Other:1

Benign, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 22, 2023	- -
not provided, no classification provided	literature only	Retina International	-	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

Severe early-childhood-onset retinal dystrophy

Pathogenic:2

Pathogenic, no assertion criteria provided	literature only	OMIM	Jun 14, 2002	- -
Established risk allele, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Jun 27, 2022	This variant was identified together with variant NM_000350.3:c.2588G>C. -

Retinal dystrophy

Benign:2

Benign, criteria provided, single submitter	research	Dept Of Ophthalmology, Nagoya University	Oct 01, 2023	- -
Likely benign, criteria provided, single submitter	clinical testing	Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg	Jan 01, 2022	- -

Stargardt disease

Pathogenic:1

Likely pathogenic, no assertion criteria provided

research

Sharon lab, Hadassah-Hebrew University Medical Center

Jun 23, 2019

- -

Stargardt disease 3

Uncertain:1

Uncertain significance, no assertion criteria provided

research

Ophthalmo-Genetics Lab, Instituto de Oftalmologia Conde de Valenciana

- -

Retinitis Pigmentosa, Recessive

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Stargardt Disease, Recessive

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

ABCA4-related disorder

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 27, 2017

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

Cone-Rod Dystrophy, Recessive

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Macular degeneration

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

MACULAR DEGENERATION, AGE-RELATED, 2, SUSCEPTIBILITY TO

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Jun 14, 2002

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.089

BayesDel_addAF

Benign

-0.28

BayesDel_noAF

Benign

-0.14

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.38

T;.

Eigen

Benign

-0.28

Eigen_PC

Benign

-0.17

FATHMM_MKL

Benign

0.51

LIST_S2

Benign

0.84

T;D

MetaRNN

Benign

0.0060

T;T

MetaSVM

Benign

-0.48

MutationAssessor

Benign

1.3

L;.

PrimateAI

Benign

0.30

PROVEAN

Benign

-1.0

N;.

REVEL

Uncertain

0.35

Sift

Benign

0.29

T;.

Sift4G

Benign

0.15

T;.

Polyphen

0.010

B;.

Vest4

0.15

MPC

0.18

ClinPred

0.0089

GERP RS

3.5

Varity_R

0.075

gMVP

0.75

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over